A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-04-01, 12:36 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data
nf-core/quantms Software Versions
nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms
| Process Name | Software | Version |
|---|---|---|
| CONSENSUSID | ConsensusID | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| EXTRACTPSMFEATURES | PSMFeatureExtractor | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| FDRCONSENSUSID | FalseDiscoveryRate | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| FILEMERGE | FileMerger | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDCONFLICTRESOLVER | IDConflictResolver | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDFILTER | IDFilter | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDMAPPER | IDMapper | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| ISOBARICANALYZER | IsobaricAnalyzer | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| MSSTATSCONVERTER | MSstatsConverter | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| MSSTATSTMT | bioconductor-msstatstmt | 2.2.0 |
| r-base | 4.1.1 | |
| PERCOLATOR | PercolatorAdapter | 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47 |
| percolator | 3.05.0, Build Date Aug 31 2020 19:03:04 | |
| PROTEININFERENCER | ProteinInference | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| PROTEINQUANTIFIER | ProteinQuantifier | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SDRFPARSING | sdrf-pipelines | 0.0.21 |
| SEARCHENGINECOMET | Comet | 2019.01 rev. 5 |
| CometAdapter | 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47 | |
| SEARCHENGINEMSGF | MSGFPlusAdapter | 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47 |
| msgf_plus | MS-GF+ Release (v2021.03.22) (22 March 2021) | |
| THERMORAWFILEPARSER | ThermoRawFileParser | 1.3.4 |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms
Core Nextflow options
- runName
- loving_cajal
- containerEngine
- singularity
- launchDir
- /hps/nobackup/juan/pride/reanalysis/PXD020248
- workDir
- /hps/nobackup/juan/pride/reanalysis/PXD020248/work
- projectDir
- /hps/nobackup/juan/pride/reanalysis/quantms
- userName
- pst_prd
- profile
- ebiclusters
- configFiles
- /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config, /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config
Input/output options
- input
- PXD020248-TMT.sdrf.tsv
- outdir
- PXD020248-TMT
- root_folder
- /hps/nobackup/juan/pride/reanalysis/PXD020248/
- local_input_type
- raw
Protein database
- database
- /hps/nobackup/juan/pride/reanalysis/multiomics-configs/databases/Homo-sapiens-uniprot-reviewed-isoforms-contaminants-decoy-202105.fasta
Database search
- search_engines
- comet,msgf
- instrument
- N/A
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- N/A
Isobaric analyzer
- select_activation
- HCD
Protein Quantification (DDA)
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- acquisition_method
- N/A
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
Statistical post-processing
- contrasts
- pairwise
Quality control
- enable_pmultiqc
- true
Max job request options
- max_cpus
- 48
- max_memory
- 300 GB
- max_time
- 10d
Generic options
- hostnames
- N/A